Mo,
AMBER does usually remove center of mass motion, but with some caveats.
I'll avoid copying and pasting the manual here, so go look for the "nscm"
flag in the manual (section 2.5.6 in the AMBER12 manual). If you are doing
a diffusion calculation, the unwrapped positions are what you want,
otherwise you are tracking the primary image particles and not the
"physical" particles.
Regards,
Brian
On Tue, Sep 18, 2012 at 3:28 PM, Mo Chen <mc842.cornell.edu> wrote:
> Dear Amber users/developers,
> I am running Langevin dynamics simulations (ntt=3) for organic solvent
> using Amber 11, and would like to calculate the self-diffusion coefficient
> from the MSD vs. tau plot. My input file has inwrap=0 (default). I wonder
> if I can use this trajectory to calculate MSD vs. tau directly? Or do I
> need to post-process the trajectory by wrapping and re-centering the
> primary box, and then unwrapping it, before the MSD calculation? In another
> word, I was wondering if AMBER removes center of mass motions automatically
> during simulation? Thank you very much in advance!
>
>
> Best,
> Mo
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>
--
================================ Current Address =======================
Brian Radak : BioMaPS
Institute for Quantitative Biology
PhD candidate - York Research Group : Rutgers, The State
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Department of Chemistry : Piscataway, NJ
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radakb.biomaps.rutgers.edu
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Received on Tue Sep 18 2012 - 13:00:03 PDT
